“MixOmicron” SARS-CoV-2 recombinant evades variant screening

During the last year of the coronavirus disease 2019 (COVID-19) pandemic, multiple variants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged and circulated, often at the same time.

This has set the stage for recombinations, which are a common feature of coronaviruses.

A new preprint describes a new variant that resembles the Omicron BA.2 for the most part, but has a small segment at the 3’ tip that belongs to the BA.1 variant. This underlines the importance of genomic surveillance in eliciting the reasons for different viral behaviors during the various waves of the pandemic.

Introduction

Earlier in 2021, the Delta variant was still circulating when the Omicron variant began to be identified and began its rise to dominance. As such, there were high chances of coinfection with both strains, which could promote homologous recombinations of genetic material between them.

In fact, the authors of the current study had already reported a couple of other recombinant SARS-CoV-2 variants, between the Alpha and B.1.160 strains and the second between the Delta and Omicron.

Both these recombinants were identified about 10 weeks after the second variant of the period began to co-circulate in the area. The current study, published on the medRxiv* preprint server, describes a third recombinant, the so-called MixOmicron.

Findings

The researchers examined nasopharyngeal samples for SARS-CoV-2 genetic material using real-time reverse transcription-PCR (qPCR). The samples came from two adult patients, with the cycle threshold values being 13 and 19, respectively. The test detected all targeted genes, including the spike K417N mutation, indicating the presence of the Omicron variant.

This was followed by next-generation sequencing, which showed the presence of a hybrid genome of Omicron 21L/BA.2-21K/BA.1. That is, while based upon the 21L/BA.2 sequence, the 3’ region for about 2,500 to 3,000 nucleotides is that of the 21K/BA.1. This region has no specifically recognizable mutations.

The recombination occurs between nucleotides 26,858 and 27,382 of the ancestral viral isolate. One specific element of the genome at this point was a short transposable element, 41 km long, called S2m, that is found in the Omicron 21K/BA.1 variant.

When it comes to the Omicron 21L/BA.2 variant, this sequence misses 26 nucleotides from the middle, and therefore is not detected by currently used tests for SARS-CoV-2 variants. Such tests are based on detecting spike mutations, or sometimes mutations in other parts of the genome.

In the majority of reads at the mutated positions in this sequence, over 98% of sequences showed the presence of the more common nucleotide, which suggests that there is a low possibility of contamination by the other variant, or of coinfection, which could otherwise explain the presence of sequences from both genomes.

Totally, the hybrid genome has 65 mutations setting it apart from the ancestral variant. Of these, 3 or 4 are not characteristic of Omicron, whether BA.1 or BA.2, while all spike mutations are identical to the Omicron mutations, except for one synonymous mutation.

Phylogenetic analysis shows that the recombinant sequences were descended from the Omicron BA.2 variant, but with a difference in the way that the whole recombinant genomes were clustered vs the two partial recombinants in this clade. The former formed separate clusters, but the latter formed a nest within it.

Implications

The study findings show that genetic recombinants are emerging within the SARS-CoV-2 variants. Earlier research has suggested that up to 5% of the circulating strains in the USA and the UK were recombinants. More and more such cases are being reported, as different variants circulate together at high rates in the same area.

In the current situation, there were over 15,000 BA.1 infections vs less than a thousand BA.2 infections in 11 weeks. As mutations accumulate, recombinants become more recognizable since the mutations occur at shorter intervals.

With the same spike protein sequence as that of Omicron BA.2, the hybrid is likely to have the same immune escape characteristics. However, the 3’ terminal sequence has been acquired from the BA.1 variant with the S2m short transposable element. Not only is this motif found in four different single-stranded RNA virus families, including all Sarbecoviruses and most SARS-CoV-2 genomes, but it is very similar to those found in insect genetic material.

The functional importance of this element may lie in its RNA interference capabilities. It is involved in the viral takeover of host protein synthesis and RNA recombination. It may also mediate pathogenicity and infection in several animal hosts. In fact, it is postulated that it interacts with a cellular miRNA in humans and thus evades detection by the host immune response.

In the few variants of SARS-CoV-2 in which S2m was absent or shortened, transmissibility was low. This is also true of Omicron BA.2, which may indicate that S2m is a virulence factor. Its presence in this hybrid BA.2-based genome could lead to a gain of viral transmissibility, which would fuel epidemic spread. Further research and surveillance would be necessary to confirm or refute this.

According to the authors,

The recombinant described here is not detected by current strategies that screen for variants in routine diagnosis by qPCR. This emphasizes the interest of the most exhaustive whole-genome based surveillance possible to allow deciphering the genetic pathways of the variability and investigating their phenotypic consequences regarding transmissibility, clinical severity, and escape from neutralizing antibodies.”

*Important notice

medRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.

Written by

Dr. Liji Thomas

Dr. Liji Thomas is an OB-GYN, who graduated from the Government Medical College, University of Calicut, Kerala, in 2001. Liji practiced as a full-time consultant in obstetrics/gynecology in a private hospital for a few years following her graduation. She has counseled hundreds of patients facing issues from pregnancy-related problems and infertility, and has been in charge of over 2,000 deliveries, striving always to achieve a normal delivery rather than operative.